Calcium in PDB 5osq: Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221)

The structure of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221), PDB code: 5osq was solved by L.Jovine, M.Monne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.90 / 2.05
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.340, 92.160, 140.950, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.1

The binding sites of Calcium atom in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221) (pdb code 5osq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221), PDB code: 5osq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:84.8 occ:1.00 O A:HOH615 2.3 74.9 1.0 O A:HOH617 2.4 56.1 1.0 OG A:SER234 2.5 73.8 1.0 O A:ASP297 2.5 75.3 1.0 O A:LYS296 2.6 89.0 1.0 O A:HOH630 2.7 55.4 1.0 HA A:ASP297 3.3 98.6 1.0 HB2 A:SER234 3.3 86.9 1.0 C A:ASP297 3.4 78.3 1.0 CB A:SER234 3.5 72.4 1.0 C A:LYS296 3.7 90.4 1.0 CA A:ASP297 3.8 82.2 1.0 HB3 A:SER234 4.1 86.9 1.0 HA A:SER234 4.1 89.9 1.0 N A:ASP297 4.3 85.4 1.0 HD3 A:LYS298 4.3 88.7 1.0 HA A:LYS298 4.4 84.2 1.0 HD3 A:PRO299 4.4 87.3 1.0 CA A:SER234 4.4 74.9 1.0 N A:LYS298 4.5 75.5 1.0 OD1 A:ASP297 4.6 74.6 1.0 HA A:LYS296 4.8 0.6 1.0 CA A:LYS296 4.9 94.7 1.0 CA A:LYS298 5.0 70.2 1.0

Calcium binding site 2 out of 6 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:65.0 occ:0.95 O B:HOH632 2.3 67.7 0.9 OD1 A:ASP185 2.4 69.3 1.0 O A:VAL182 2.4 59.4 1.0 O A:HOH670 2.4 64.9 0.9 OE1 A:GLN366 2.4 68.9 1.0 O A:HOH681 2.6 53.3 0.9 CG A:ASP185 3.1 69.0 1.0 OD2 A:ASP185 3.1 66.5 1.0 CD A:GLN366 3.3 62.1 1.0 C A:VAL182 3.6 56.8 1.0 H A:VAL182 3.7 68.5 1.0 HB2 A:GLN366 3.8 63.8 1.0 HG2 A:GLN366 3.8 67.9 1.0 O A:HOH672 4.0 58.3 0.9 HA2 A:GLY183 4.0 63.9 1.0 CG A:GLN366 4.0 56.6 1.0 HB A:VAL182 4.1 61.4 1.0 H A:ASP185 4.1 81.1 1.0 NE2 A:GLN366 4.2 58.4 1.0 N A:VAL182 4.2 57.1 1.0 HE22 A:GLN366 4.2 70.0 1.0 CA A:VAL182 4.4 52.2 1.0 CB A:GLN366 4.5 53.1 1.0 OE1 B:GLU310 4.5 86.8 1.0 CB A:ASP185 4.5 65.9 1.0 H A:VAL184 4.6 65.6 1.0 N A:GLY183 4.6 55.6 1.0 CA A:GLY183 4.7 53.3 1.0 CB A:VAL182 4.8 51.1 1.0 HA A:ASP181 4.8 71.4 1.0 OD1 A:ASP181 4.8 62.9 1.0 N A:ASP185 4.8 67.5 1.0 HB3 A:ASP185 4.8 79.1 1.0 HE21 A:GLN366 4.9 70.0 1.0 HG3 A:GLN366 4.9 67.9 1.0

Calcium binding site 3 out of 6 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.8 occ:0.93 OD2 A:ASP437 2.5 88.7 1.0 OD2 A:ASP210 2.5 68.4 1.0 O A:HOH638 2.5 58.5 0.9 OG A:SER212 2.6 65.3 1.0 OD1 A:ASP437 3.1 94.3 1.0 CG A:ASP437 3.2 87.7 1.0 CG A:ASP210 3.4 64.4 1.0 HB3 A:SER212 3.7 79.8 1.0 OD1 A:ASP210 3.7 71.1 1.0 CB A:SER212 3.7 66.5 1.0 H A:SER212 4.0 70.8 1.0 HB2 A:SER212 4.2 79.8 1.0 HG13 A:ILE213 4.3 68.5 1.0 HB2 A:LYS436 4.5 0.9 1.0 H A:ILE213 4.6 72.2 1.0 HB2 A:ASP210 4.6 66.3 1.0 CB A:ASP437 4.6 77.1 1.0 CB A:ASP210 4.6 55.3 1.0 N A:SER212 4.7 59.0 1.0 CA A:SER212 4.8 63.4 1.0 HB3 A:LYS436 4.8 0.9 1.0 HB2 A:ASP437 4.9 92.6 1.0 HB3 A:ASP437 5.0 92.6 1.0 HB3 A:ASP210 5.0 66.3 1.0

Calcium binding site 4 out of 6 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:77.8 occ:1.00 O B:HOH606 2.3 57.0 1.0 OG B:SER234 2.4 64.9 1.0 O B:HOH735 2.4 54.0 1.0 O B:HOH683 2.5 46.8 1.0 O B:ASP297 2.5 50.9 1.0 O B:LYS296 2.7 60.8 1.0 HA B:ASP297 3.1 72.1 1.0 C B:ASP297 3.4 51.7 1.0 HB2 B:SER234 3.6 79.0 1.0 CB B:SER234 3.6 65.9 1.0 CA B:ASP297 3.7 60.1 1.0 C B:LYS296 3.8 63.3 1.0 HB3 B:SER234 4.2 79.0 1.0 N B:ASP297 4.2 60.3 1.0 HD3 B:LYS298 4.3 69.0 1.0 OD1 B:ASP297 4.4 63.4 1.0 HA B:SER234 4.4 79.3 1.0 CA B:SER234 4.6 66.1 1.0 N B:LYS298 4.6 50.6 1.0 HA B:LYS298 4.6 61.0 1.0 HD3 B:PRO299 4.8 61.7 1.0 CB B:ASP297 5.0 59.0 1.0

Calcium binding site 5 out of 6 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:0.7 occ:0.98 OD1 B:ASP185 2.4 88.4 1.0 OE1 B:GLN366 2.4 89.5 1.0 O B:HOH630 2.5 59.1 1.0 O B:VAL182 2.6 60.0 1.0 CD B:GLN366 3.2 84.7 1.0 CG B:ASP185 3.2 84.2 1.0 OD2 B:ASP185 3.4 87.2 1.0 C B:VAL182 3.8 51.8 1.0 HG2 B:GLN366 3.8 90.7 1.0 H B:VAL182 3.8 66.8 1.0 NE2 B:GLN366 4.0 83.2 1.0 HE22 B:GLN366 4.0 99.8 1.0 HB2 B:GLN366 4.0 77.6 1.0 CG B:GLN366 4.0 75.6 1.0 HA2 B:GLY183 4.1 72.5 1.0 H B:ASP185 4.1 75.1 1.0 HB B:VAL182 4.2 50.2 1.0 N B:VAL182 4.3 55.7 1.0 CA B:VAL182 4.6 50.8 1.0 CB B:GLN366 4.6 64.6 1.0 CB B:ASP185 4.7 74.5 1.0 HE21 B:GLN366 4.7 99.8 1.0 H B:VAL184 4.7 61.5 1.0 N B:GLY183 4.8 57.9 1.0 CA B:GLY183 4.8 60.4 1.0 HA B:ASP181 4.9 74.5 1.0 HG3 B:GLN366 4.9 90.7 1.0 N B:ASP185 4.9 62.6 1.0 CB B:VAL182 4.9 41.9 1.0 OD1 B:ASP181 4.9 63.8 1.0

Calcium binding site 6 out of 6 in the Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Zp-N Domain of Mammalian Sperm Receptor ZP3 (Crystal Form II, Processed in P21221) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:83.9 occ:1.00 O B:HOH766 2.3 70.8 1.0 O B:THR54 2.4 55.5 1.0 O B:HOH751 2.4 71.1 1.0 O B:HOH662 2.7 49.9 1.0 HE2 B:LYS2 3.4 0.8 1.0 HA3 B:GLY55 3.4 63.3 1.0 C B:THR54 3.6 49.3 1.0 HB B:THR54 4.1 51.1 1.0 O B:HOH774 4.2 42.8 1.0 CA B:GLY55 4.2 52.8 1.0 HG2 B:LYS2 4.3 0.9 1.0 OD1 B:ASP56 4.3 71.4 1.0 CE B:LYS2 4.3 0.3 1.0 N B:GLY55 4.4 49.8 1.0 HA B:THR54 4.6 53.4 1.0 CA B:THR54 4.6 44.5 1.0 OD2 B:ASP56 4.7 68.9 1.0 C B:GLY55 4.7 50.8 1.0 HE3 B:LYS2 4.7 0.8 1.0 CB B:THR54 4.8 42.5 1.0 CG B:ASP56 4.8 65.4 1.0 HZ1 B:LYS2 4.8 0.5 1.0 HZ3 B:LYS2 4.9 0.5 1.0 NZ B:LYS2 5.0 0.1 1.0 HA2 B:GLY55 5.0 63.3 1.0 HD3 B:LYS2 5.0 0.9 1.0

M.Monne, L.Han, T.Schwend, S.Burendahl, L.Jovine. Crystal Structure of the Zp-N Domain of ZP3 Reveals the Core Fold of Animal Egg Coats Nature V. 456 653 2008.
ISSN: ISSN 0028-0836
PubMed: 19052627
DOI: 10.1038/NATURE07599